data_6JBF # _entry.id 6JBF # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 6JBF pdb_00006jbf 10.2210/pdb6jbf/pdb WWPDB D_1300010796 ? ? # _pdbx_database_PDB_obs_spr.id SPRSDE _pdbx_database_PDB_obs_spr.date 2020-01-29 _pdbx_database_PDB_obs_spr.pdb_id 6JBF _pdbx_database_PDB_obs_spr.replace_pdb_id 5BWS _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6JBF _pdbx_database_status.recvd_initial_deposition_date 2019-01-25 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kanazawa, H.' 1 ? 'Auffinger, P.' 2 ? 'Hanessian, S.' 3 ? 'Kondo, J.' 4 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title ;Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F) ; _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Hanessian, S.' 2 ? primary 'Kanazawa, H.' 3 ? # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 95.280 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 6JBF _cell.details ? _cell.formula_units_Z ? _cell.length_a 27.111 _cell.length_a_esd ? _cell.length_b 81.324 _cell.length_b_esd ? _cell.length_c 50.131 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JBF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3') ; 7370.424 4 ? ? ? ? 2 non-polymer syn '(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranoside' 324.349 1 ? ? ? ? 3 water nat water 18.015 95 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code UUGCGUCACGCCGGCGAAGUCGC _entity_poly.pdbx_seq_one_letter_code_can UUGCGUCACGCCGGCGAAGUCGC _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 U n 1 3 G n 1 4 C n 1 5 G n 1 6 U n 1 7 C n 1 8 A n 1 9 C n 1 10 G n 1 11 C n 1 12 C n 1 13 G n 1 14 G n 1 15 C n 1 16 G n 1 17 A n 1 18 A n 1 19 G n 1 20 U n 1 21 C n 1 22 G n 1 23 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 23 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6JBF _struct_ref.pdbx_db_accession 6JBF _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 6JBF A 1 ? 23 ? 6JBF 1 ? 23 ? 1 23 2 1 6JBF B 1 ? 23 ? 6JBF 24 ? 46 ? 24 46 3 1 6JBF C 1 ? 23 ? 6JBF 47 ? 69 ? 47 69 4 1 6JBF D 1 ? 23 ? 6JBF 70 ? 92 ? 70 92 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 V71 D-saccharide . '(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranoside' ;(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactoside; (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-D-galactoside; (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-galactoside ; 'C12 H25 F N4 O5' 324.349 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 6JBF _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 34.10 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'PEG 3350, NaCl, spermine tetrahydrochloride, sodium cacodylate' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 270' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-12-09 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.98 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-17A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.98 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-17A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate 35.080 _reflns.entry_id 6JBF _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.6 _reflns.d_resolution_low 42.543 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 6744 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.800 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.782 _reflns.pdbx_Rmerge_I_obs 0.056 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 25.150 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 0.993 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.061 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_R_split ? _reflns.pdbx_CC_star ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_R_split _reflns_shell.pdbx_CC_star 2.600 2.660 ? 7.630 ? ? ? ? 493 98.600 ? ? ? ? 0.281 ? ? ? ? ? ? ? ? 6.850 ? ? ? ? 0.305 ? ? 1 1 0.962 ? ? 2.660 2.740 ? 8.150 ? ? ? ? 495 100.000 ? ? ? ? 0.244 ? ? ? ? ? ? ? ? 6.602 ? ? ? ? 0.265 ? ? 2 1 0.976 ? ? 2.740 2.820 ? 10.490 ? ? ? ? 459 100.000 ? ? ? ? 0.191 ? ? ? ? ? ? ? ? 7.033 ? ? ? ? 0.207 ? ? 3 1 0.983 ? ? 2.820 2.900 ? 13.430 ? ? ? ? 453 99.600 ? ? ? ? 0.143 ? ? ? ? ? ? ? ? 7.018 ? ? ? ? 0.154 ? ? 4 1 0.995 ? ? 2.900 3.000 ? 15.740 ? ? ? ? 455 100.000 ? ? ? ? 0.110 ? ? ? ? ? ? ? ? 6.776 ? ? ? ? 0.119 ? ? 5 1 0.996 ? ? 3.000 3.100 ? 20.660 ? ? ? ? 424 100.000 ? ? ? ? 0.072 ? ? ? ? ? ? ? ? 6.811 ? ? ? ? 0.078 ? ? 6 1 0.999 ? ? 3.100 3.220 ? 23.720 ? ? ? ? 411 100.000 ? ? ? ? 0.062 ? ? ? ? ? ? ? ? 6.903 ? ? ? ? 0.067 ? ? 7 1 0.999 ? ? 3.220 3.350 ? 23.410 ? ? ? ? 414 100.000 ? ? ? ? 0.064 ? ? ? ? ? ? ? ? 6.633 ? ? ? ? 0.069 ? ? 8 1 0.999 ? ? 3.350 3.500 ? 26.870 ? ? ? ? 377 99.700 ? ? ? ? 0.055 ? ? ? ? ? ? ? ? 7.090 ? ? ? ? 0.060 ? ? 9 1 0.999 ? ? 3.500 3.670 ? 27.310 ? ? ? ? 358 100.000 ? ? ? ? 0.056 ? ? ? ? ? ? ? ? 6.832 ? ? ? ? 0.061 ? ? 10 1 0.999 ? ? 3.670 3.870 ? 29.690 ? ? ? ? 365 99.700 ? ? ? ? 0.047 ? ? ? ? ? ? ? ? 6.455 ? ? ? ? 0.051 ? ? 11 1 0.999 ? ? 3.870 4.100 ? 36.820 ? ? ? ? 309 99.700 ? ? ? ? 0.043 ? ? ? ? ? ? ? ? 6.864 ? ? ? ? 0.047 ? ? 12 1 0.999 ? ? 4.100 4.390 ? 38.330 ? ? ? ? 312 99.400 ? ? ? ? 0.041 ? ? ? ? ? ? ? ? 6.596 ? ? ? ? 0.045 ? ? 13 1 0.998 ? ? 4.390 4.740 ? 37.260 ? ? ? ? 288 100.000 ? ? ? ? 0.043 ? ? ? ? ? ? ? ? 6.868 ? ? ? ? 0.047 ? ? 14 1 0.999 ? ? 4.740 5.190 ? 42.370 ? ? ? ? 265 100.000 ? ? ? ? 0.038 ? ? ? ? ? ? ? ? 6.506 ? ? ? ? 0.042 ? ? 15 1 0.999 ? ? 5.190 5.800 ? 45.540 ? ? ? ? 244 100.000 ? ? ? ? 0.035 ? ? ? ? ? ? ? ? 6.844 ? ? ? ? 0.037 ? ? 16 1 0.999 ? ? 5.800 6.700 ? 42.880 ? ? ? ? 221 100.000 ? ? ? ? 0.034 ? ? ? ? ? ? ? ? 6.756 ? ? ? ? 0.037 ? ? 17 1 0.999 ? ? 6.700 8.210 ? 45.780 ? ? ? ? 177 98.900 ? ? ? ? 0.032 ? ? ? ? ? ? ? ? 6.627 ? ? ? ? 0.034 ? ? 18 1 0.999 ? ? 8.210 11.610 ? 45.860 ? ? ? ? 141 100.000 ? ? ? ? 0.028 ? ? ? ? ? ? ? ? 6.574 ? ? ? ? 0.030 ? ? 19 1 1.000 ? ? 11.610 42.543 ? 52.120 ? ? ? ? 83 98.800 ? ? ? ? 0.022 ? ? ? ? ? ? ? ? 6.169 ? ? ? ? 0.024 ? ? 20 1 1.000 ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max 76.410 _refine.B_iso_mean 32.5800 _refine.B_iso_min 13.730 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 6JBF _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.6 _refine.ls_d_res_low 42.5430 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 6718 _refine.ls_number_reflns_R_free 670 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.4400 _refine.ls_percent_reflns_R_free 9.9700 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1613 _refine.ls_R_factor_R_free 0.2290 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1538 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.380 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 1J7T _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 24.9400 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.3600 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 2.6 _refine_hist.d_res_low 42.5430 _refine_hist.pdbx_number_atoms_ligand 22 _refine_hist.number_atoms_solvent 95 _refine_hist.number_atoms_total 2065 _refine_hist.pdbx_number_residues_total 92 _refine_hist.pdbx_B_iso_mean_ligand 23.30 _refine_hist.pdbx_B_iso_mean_solvent 30.02 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1948 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.009 ? 2197 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.053 ? 3414 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.044 ? 466 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.006 ? 92 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 9.875 ? 1088 ? f_dihedral_angle_d ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.5954 2.7957 1342 . 139 1203 100.0000 . . . 0.3822 0.0000 0.2489 . . . . . . 5 . . . 'X-RAY DIFFRACTION' 2.7957 3.0770 1343 . 133 1210 100.0000 . . . 0.2972 0.0000 0.2045 . . . . . . 5 . . . 'X-RAY DIFFRACTION' 3.0770 3.5221 1324 . 140 1184 99.0000 . . . 0.2468 0.0000 0.1633 . . . . . . 5 . . . 'X-RAY DIFFRACTION' 3.5221 4.4367 1345 . 129 1216 99.0000 . . . 0.1876 0.0000 0.1232 . . . . . . 5 . . . 'X-RAY DIFFRACTION' 4.4367 42.5485 1364 . 129 1235 99.0000 . . . 0.1698 0.0000 0.1226 . . . . . . 5 . . . # _struct.entry_id 6JBF _struct.title ;Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F) ; _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 6JBF _struct_keywords.text 'RNA, antibiotic, RNA-ANTIBIOTIC complex' _struct_keywords.pdbx_keywords RNA/ANTIBIOTIC # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 1 ? E N N 2 ? F N N 3 ? G N N 3 ? H N N 3 ? I N N 3 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 23 N3 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 23 O2 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 23 N4 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 22 N1 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 22 O6 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 22 N2 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 21 N3 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 6 N3 ? ? ? 1_555 B U 20 O4 ? ? A U 6 B U 43 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog11 hydrog ? ? A U 6 O2 ? ? ? 1_555 B U 20 N3 ? ? A U 6 B U 43 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog12 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 16 N1 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 16 O6 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 16 N2 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 10 N1 ? ? ? 1_555 B C 15 N3 ? ? A G 10 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 N2 ? ? ? 1_555 B C 15 O2 ? ? A G 10 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 10 O6 ? ? ? 1_555 B C 15 N4 ? ? A G 10 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 14 N1 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 14 O6 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 14 N2 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 15 B G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 15 B G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 15 B G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 16 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 16 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 16 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A A 18 N6 ? ? ? 1_555 B A 8 N1 ? ? A A 18 B A 31 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog40 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A U 20 N3 ? ? ? 1_555 B U 6 O2 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog44 hydrog ? ? A U 20 O4 ? ? ? 1_555 B U 6 N3 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog45 hydrog ? ? A C 21 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 21 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 22 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 22 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A G 22 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 23 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A C 23 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A C 23 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C G 3 N1 ? ? ? 1_555 D C 23 N3 ? ? C G 49 D C 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C G 3 N2 ? ? ? 1_555 D C 23 O2 ? ? C G 49 D C 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? C G 3 O6 ? ? ? 1_555 D C 23 N4 ? ? C G 49 D C 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? C C 4 N3 ? ? ? 1_555 D G 22 N1 ? ? C C 50 D G 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? C C 4 N4 ? ? ? 1_555 D G 22 O6 ? ? C C 50 D G 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? C C 4 O2 ? ? ? 1_555 D G 22 N2 ? ? C C 50 D G 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? C G 5 N1 ? ? ? 1_555 D C 21 N3 ? ? C G 51 D C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? C G 5 N2 ? ? ? 1_555 D C 21 O2 ? ? C G 51 D C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? C G 5 O6 ? ? ? 1_555 D C 21 N4 ? ? C G 51 D C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? C U 6 N3 ? ? ? 1_555 D U 20 O4 ? ? C U 52 D U 89 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog64 hydrog ? ? C U 6 O2 ? ? ? 1_555 D U 20 N3 ? ? C U 52 D U 89 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog65 hydrog ? ? C C 7 N3 ? ? ? 1_555 D G 19 N1 ? ? C C 53 D G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? C C 7 N4 ? ? ? 1_555 D G 19 O6 ? ? C C 53 D G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? C C 7 O2 ? ? ? 1_555 D G 19 N2 ? ? C C 53 D G 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? C A 8 N1 ? ? ? 1_555 D A 17 N6 ? ? C A 54 D A 86 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog69 hydrog ? ? C A 8 N1 ? ? ? 1_555 D A 18 N6 ? ? C A 54 D A 87 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog70 hydrog ? ? C C 9 N3 ? ? ? 1_555 D G 16 N1 ? ? C C 55 D G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? C C 9 N4 ? ? ? 1_555 D G 16 O6 ? ? C C 55 D G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? C C 9 O2 ? ? ? 1_555 D G 16 N2 ? ? C C 55 D G 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? C G 10 N1 ? ? ? 1_555 D C 15 N3 ? ? C G 56 D C 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? C G 10 N2 ? ? ? 1_555 D C 15 O2 ? ? C G 56 D C 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? C G 10 O6 ? ? ? 1_555 D C 15 N4 ? ? C G 56 D C 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? C C 11 N3 ? ? ? 1_555 D G 14 N1 ? ? C C 57 D G 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? C C 11 N4 ? ? ? 1_555 D G 14 O6 ? ? C C 57 D G 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? C C 11 O2 ? ? ? 1_555 D G 14 N2 ? ? C C 57 D G 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? C C 12 N3 ? ? ? 1_555 D G 13 N1 ? ? C C 58 D G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? C C 12 N4 ? ? ? 1_555 D G 13 O6 ? ? C C 58 D G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? C C 12 O2 ? ? ? 1_555 D G 13 N2 ? ? C C 58 D G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog82 hydrog ? ? C G 13 N1 ? ? ? 1_555 D C 12 N3 ? ? C G 59 D C 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog83 hydrog ? ? C G 13 N2 ? ? ? 1_555 D C 12 O2 ? ? C G 59 D C 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? C G 13 O6 ? ? ? 1_555 D C 12 N4 ? ? C G 59 D C 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog85 hydrog ? ? C G 14 N1 ? ? ? 1_555 D C 11 N3 ? ? C G 60 D C 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? C G 14 N2 ? ? ? 1_555 D C 11 O2 ? ? C G 60 D C 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog87 hydrog ? ? C G 14 O6 ? ? ? 1_555 D C 11 N4 ? ? C G 60 D C 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog88 hydrog ? ? C C 15 N3 ? ? ? 1_555 D G 10 N1 ? ? C C 61 D G 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog89 hydrog ? ? C C 15 N4 ? ? ? 1_555 D G 10 O6 ? ? C C 61 D G 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog90 hydrog ? ? C C 15 O2 ? ? ? 1_555 D G 10 N2 ? ? C C 61 D G 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog91 hydrog ? ? C G 16 N1 ? ? ? 1_555 D C 9 N3 ? ? C G 62 D C 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog92 hydrog ? ? C G 16 N2 ? ? ? 1_555 D C 9 O2 ? ? C G 62 D C 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog93 hydrog ? ? C G 16 O6 ? ? ? 1_555 D C 9 N4 ? ? C G 62 D C 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog94 hydrog ? ? C A 17 N6 ? ? ? 1_555 D A 8 N1 ? ? C A 63 D A 77 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog95 hydrog ? ? C A 17 N6 ? ? ? 1_555 D C 9 O2 ? ? C A 63 D C 78 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog96 hydrog ? ? C A 18 N6 ? ? ? 1_555 D A 8 N1 ? ? C A 64 D A 77 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog97 hydrog ? ? C G 19 N1 ? ? ? 1_555 D C 7 N3 ? ? C G 65 D C 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog98 hydrog ? ? C G 19 N2 ? ? ? 1_555 D C 7 O2 ? ? C G 65 D C 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog99 hydrog ? ? C G 19 O6 ? ? ? 1_555 D C 7 N4 ? ? C G 65 D C 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog100 hydrog ? ? C U 20 N3 ? ? ? 1_555 D U 6 O2 ? ? C U 66 D U 75 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog101 hydrog ? ? C U 20 O4 ? ? ? 1_555 D U 6 N3 ? ? C U 66 D U 75 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog102 hydrog ? ? C C 21 N3 ? ? ? 1_555 D G 5 N1 ? ? C C 67 D G 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog103 hydrog ? ? C C 21 N4 ? ? ? 1_555 D G 5 O6 ? ? C C 67 D G 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog104 hydrog ? ? C C 21 O2 ? ? ? 1_555 D G 5 N2 ? ? C C 67 D G 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog105 hydrog ? ? C G 22 N1 ? ? ? 1_555 D C 4 N3 ? ? C G 68 D C 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog106 hydrog ? ? C G 22 N2 ? ? ? 1_555 D C 4 O2 ? ? C G 68 D C 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog107 hydrog ? ? C G 22 O6 ? ? ? 1_555 D C 4 N4 ? ? C G 68 D C 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog108 hydrog ? ? C C 23 N3 ? ? ? 1_555 D G 3 N1 ? ? C C 69 D G 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog109 hydrog ? ? C C 23 N4 ? ? ? 1_555 D G 3 O6 ? ? C C 69 D G 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog110 hydrog ? ? C C 23 O2 ? ? ? 1_555 D G 3 N2 ? ? C C 69 D G 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 6JBF _atom_sites.fract_transf_matrix[1][1] 0.036885 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.003412 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.012296 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.020033 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C F N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 U 1 1 1 U U A . n A 1 2 U 2 2 2 U U A . n A 1 3 G 3 3 3 G G A . n A 1 4 C 4 4 4 C C A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 A 8 8 8 A A A . n A 1 9 C 9 9 9 C C A . n A 1 10 G 10 10 10 G G A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 G 13 13 13 G G A . n A 1 14 G 14 14 14 G G A . n A 1 15 C 15 15 15 C C A . n A 1 16 G 16 16 16 G G A . n A 1 17 A 17 17 17 A A A . n A 1 18 A 18 18 18 A A A . n A 1 19 G 19 19 19 G G A . n A 1 20 U 20 20 20 U U A . n A 1 21 C 21 21 21 C C A . n A 1 22 G 22 22 22 G G A . n A 1 23 C 23 23 23 C C A . n B 1 1 U 1 24 24 U U B . n B 1 2 U 2 25 25 U U B . n B 1 3 G 3 26 26 G G B . n B 1 4 C 4 27 27 C C B . n B 1 5 G 5 28 28 G G B . n B 1 6 U 6 29 29 U U B . n B 1 7 C 7 30 30 C C B . n B 1 8 A 8 31 31 A A B . n B 1 9 C 9 32 32 C C B . n B 1 10 G 10 33 33 G G B . n B 1 11 C 11 34 34 C C B . n B 1 12 C 12 35 35 C C B . n B 1 13 G 13 36 36 G G B . n B 1 14 G 14 37 37 G G B . n B 1 15 C 15 38 38 C C B . n B 1 16 G 16 39 39 G G B . n B 1 17 A 17 40 40 A A B . n B 1 18 A 18 41 41 A A B . n B 1 19 G 19 42 42 G G B . n B 1 20 U 20 43 43 U U B . n B 1 21 C 21 44 44 C C B . n B 1 22 G 22 45 45 G G B . n B 1 23 C 23 46 46 C C B . n C 1 1 U 1 47 47 U U C . n C 1 2 U 2 48 48 U U C . n C 1 3 G 3 49 49 G G C . n C 1 4 C 4 50 50 C C C . n C 1 5 G 5 51 51 G G C . n C 1 6 U 6 52 52 U U C . n C 1 7 C 7 53 53 C C C . n C 1 8 A 8 54 54 A A C . n C 1 9 C 9 55 55 C C C . n C 1 10 G 10 56 56 G G C . n C 1 11 C 11 57 57 C C C . n C 1 12 C 12 58 58 C C C . n C 1 13 G 13 59 59 G G C . n C 1 14 G 14 60 60 G G C . n C 1 15 C 15 61 61 C C C . n C 1 16 G 16 62 62 G G C . n C 1 17 A 17 63 63 A A C . n C 1 18 A 18 64 64 A A C . n C 1 19 G 19 65 65 G G C . n C 1 20 U 20 66 66 U U C . n C 1 21 C 21 67 67 C C C . n C 1 22 G 22 68 68 G G C . n C 1 23 C 23 69 69 C C C . n D 1 1 U 1 70 70 U U D . n D 1 2 U 2 71 71 U U D . n D 1 3 G 3 72 72 G G D . n D 1 4 C 4 73 73 C C D . n D 1 5 G 5 74 74 G G D . n D 1 6 U 6 75 75 U U D . n D 1 7 C 7 76 76 C C D . n D 1 8 A 8 77 77 A A D . n D 1 9 C 9 78 78 C C D . n D 1 10 G 10 79 79 G G D . n D 1 11 C 11 80 80 C C D . n D 1 12 C 12 81 81 C C D . n D 1 13 G 13 82 82 G G D . n D 1 14 G 14 83 83 G G D . n D 1 15 C 15 84 84 C C D . n D 1 16 G 16 85 85 G G D . n D 1 17 A 17 86 86 A A D . n D 1 18 A 18 87 87 A A D . n D 1 19 G 19 88 88 G G D . n D 1 20 U 20 89 89 U U D . n D 1 21 C 21 90 90 C C D . n D 1 22 G 22 91 91 G G D . n D 1 23 C 23 92 92 C C D . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 2 V71 1 100 100 V71 V71 B . F 3 HOH 1 101 118 HOH HOH A . F 3 HOH 2 102 134 HOH HOH A . F 3 HOH 3 103 172 HOH HOH A . F 3 HOH 4 104 153 HOH HOH A . F 3 HOH 5 105 145 HOH HOH A . F 3 HOH 6 106 169 HOH HOH A . F 3 HOH 7 107 147 HOH HOH A . F 3 HOH 8 108 152 HOH HOH A . F 3 HOH 9 109 127 HOH HOH A . F 3 HOH 10 110 112 HOH HOH A . F 3 HOH 11 111 149 HOH HOH A . F 3 HOH 12 112 131 HOH HOH A . F 3 HOH 13 113 154 HOH HOH A . F 3 HOH 14 114 140 HOH HOH A . F 3 HOH 15 115 193 HOH HOH A . F 3 HOH 16 116 129 HOH HOH A . F 3 HOH 17 117 157 HOH HOH A . F 3 HOH 18 118 171 HOH HOH A . F 3 HOH 19 119 110 HOH HOH A . F 3 HOH 20 120 166 HOH HOH A . F 3 HOH 21 121 190 HOH HOH A . F 3 HOH 22 122 123 HOH HOH A . F 3 HOH 23 123 185 HOH HOH A . F 3 HOH 24 124 161 HOH HOH A . F 3 HOH 25 125 159 HOH HOH A . G 3 HOH 1 201 128 HOH HOH B . G 3 HOH 2 202 184 HOH HOH B . G 3 HOH 3 203 148 HOH HOH B . G 3 HOH 4 204 163 HOH HOH B . G 3 HOH 5 205 108 HOH HOH B . G 3 HOH 6 206 107 HOH HOH B . G 3 HOH 7 207 182 HOH HOH B . G 3 HOH 8 208 137 HOH HOH B . G 3 HOH 9 209 122 HOH HOH B . G 3 HOH 10 210 117 HOH HOH B . G 3 HOH 11 211 105 HOH HOH B . G 3 HOH 12 212 151 HOH HOH B . G 3 HOH 13 213 136 HOH HOH B . G 3 HOH 14 214 116 HOH HOH B . G 3 HOH 15 215 111 HOH HOH B . G 3 HOH 16 216 121 HOH HOH B . G 3 HOH 17 217 168 HOH HOH B . G 3 HOH 18 218 165 HOH HOH B . G 3 HOH 19 219 191 HOH HOH B . G 3 HOH 20 220 162 HOH HOH B . G 3 HOH 21 221 186 HOH HOH B . G 3 HOH 22 222 167 HOH HOH B . G 3 HOH 23 223 164 HOH HOH B . G 3 HOH 24 224 192 HOH HOH B . G 3 HOH 25 225 195 HOH HOH B . H 3 HOH 1 101 109 HOH HOH C . H 3 HOH 2 102 158 HOH HOH C . H 3 HOH 3 103 115 HOH HOH C . H 3 HOH 4 104 101 HOH HOH C . H 3 HOH 5 105 178 HOH HOH C . H 3 HOH 6 106 183 HOH HOH C . H 3 HOH 7 107 144 HOH HOH C . H 3 HOH 8 108 104 HOH HOH C . H 3 HOH 9 109 113 HOH HOH C . H 3 HOH 10 110 138 HOH HOH C . H 3 HOH 11 111 177 HOH HOH C . H 3 HOH 12 112 132 HOH HOH C . H 3 HOH 13 113 120 HOH HOH C . H 3 HOH 14 114 125 HOH HOH C . H 3 HOH 15 115 126 HOH HOH C . H 3 HOH 16 116 133 HOH HOH C . H 3 HOH 17 117 180 HOH HOH C . H 3 HOH 18 118 170 HOH HOH C . H 3 HOH 19 119 142 HOH HOH C . H 3 HOH 20 120 181 HOH HOH C . H 3 HOH 21 121 179 HOH HOH C . H 3 HOH 22 122 156 HOH HOH C . H 3 HOH 23 123 187 HOH HOH C . H 3 HOH 24 124 189 HOH HOH C . I 3 HOH 1 101 102 HOH HOH D . I 3 HOH 2 102 103 HOH HOH D . I 3 HOH 3 103 150 HOH HOH D . I 3 HOH 4 104 124 HOH HOH D . I 3 HOH 5 105 143 HOH HOH D . I 3 HOH 6 106 194 HOH HOH D . I 3 HOH 7 107 106 HOH HOH D . I 3 HOH 8 108 130 HOH HOH D . I 3 HOH 9 109 139 HOH HOH D . I 3 HOH 10 110 146 HOH HOH D . I 3 HOH 11 111 119 HOH HOH D . I 3 HOH 12 112 135 HOH HOH D . I 3 HOH 13 113 174 HOH HOH D . I 3 HOH 14 114 114 HOH HOH D . I 3 HOH 15 115 173 HOH HOH D . I 3 HOH 16 116 141 HOH HOH D . I 3 HOH 17 117 176 HOH HOH D . I 3 HOH 18 118 160 HOH HOH D . I 3 HOH 19 119 175 HOH HOH D . I 3 HOH 20 120 155 HOH HOH D . I 3 HOH 21 121 188 HOH HOH D . # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 author_and_software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E,F,G 2 1 C,D,H,I # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2450 ? 1 MORE -14 ? 1 'SSA (A^2)' 8230 ? 2 'ABSA (A^2)' 2080 ? 2 MORE -18 ? 2 'SSA (A^2)' 8340 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2020-01-29 2 'Structure model' 1 1 2020-03-25 3 'Structure model' 2 0 2020-07-29 4 'Structure model' 2 1 2023-11-22 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 3 'Structure model' repository Remediation 'Carbohydrate remediation' ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 3 'Structure model' 'Atomic model' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 4 'Structure model' 'Refinement description' 8 4 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' reflns_shell 2 3 'Structure model' atom_site 3 3 'Structure model' chem_comp 4 3 'Structure model' struct_site 5 3 'Structure model' struct_site_gen 6 4 'Structure model' chem_comp 7 4 'Structure model' chem_comp_atom 8 4 'Structure model' chem_comp_bond 9 4 'Structure model' database_2 10 4 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_reflns_shell.percent_possible_all' 2 3 'Structure model' '_atom_site.auth_atom_id' 3 3 'Structure model' '_atom_site.label_atom_id' 4 3 'Structure model' '_chem_comp.type' 5 4 'Structure model' '_chem_comp.pdbx_synonyms' 6 4 'Structure model' '_database_2.pdbx_DOI' 7 4 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.8.3_1479 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.24 3 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" C C 58 ? ? P C G 59 ? ? 1.505 1.607 -0.102 0.012 Y 2 1 "O3'" C A 63 ? ? P C A 64 ? ? 1.529 1.607 -0.078 0.012 Y # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 U OP3 O N N 114 U P P N N 115 U OP1 O N N 116 U OP2 O N N 117 U "O5'" O N N 118 U "C5'" C N N 119 U "C4'" C N R 120 U "O4'" O N N 121 U "C3'" C N S 122 U "O3'" O N N 123 U "C2'" C N R 124 U "O2'" O N N 125 U "C1'" C N R 126 U N1 N N N 127 U C2 C N N 128 U O2 O N N 129 U N3 N N N 130 U C4 C N N 131 U O4 O N N 132 U C5 C N N 133 U C6 C N N 134 U HOP3 H N N 135 U HOP2 H N N 136 U "H5'" H N N 137 U "H5''" H N N 138 U "H4'" H N N 139 U "H3'" H N N 140 U "HO3'" H N N 141 U "H2'" H N N 142 U "HO2'" H N N 143 U "H1'" H N N 144 U H3 H N N 145 U H5 H N N 146 U H6 H N N 147 V71 C1 C N S 148 V71 C10 C N R 149 V71 C11 C N R 150 V71 C12 C N S 151 V71 C2 C N R 152 V71 C3 C N R 153 V71 C4 C N R 154 V71 C5 C N R 155 V71 C6 C N N 156 V71 C7 C N R 157 V71 C8 C N N 158 V71 C9 C N S 159 V71 F99 F N N 160 V71 N2 N N N 161 V71 N6 N N N 162 V71 N7 N N N 163 V71 N9 N N N 164 V71 O1 O N N 165 V71 O11 O N N 166 V71 O12 O N N 167 V71 O3 O N N 168 V71 O5 O N N 169 V71 H1 H N N 170 V71 H2A H N N 171 V71 H3A H N N 172 V71 H4A H N N 173 V71 H2 H N N 174 V71 H3 H N N 175 V71 H4 H N N 176 V71 H5 H N N 177 V71 H61 H N N 178 V71 H62 H N N 179 V71 H11 H N N 180 V71 H12 H N N 181 V71 H13 H N N 182 V71 H14 H N N 183 V71 H15 H N N 184 V71 H16 H N N 185 V71 H18 H N N 186 V71 H19 H N N 187 V71 H21 H N N 188 V71 H22 H N N 189 V71 H24 H N N 190 V71 H25 H N N 191 V71 H27 H N N 192 V71 H28 H N N 193 V71 HO3 H N N 194 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 V71 N6 C6 sing N N 153 V71 C6 C5 sing N N 154 V71 F99 C4 sing N N 155 V71 O5 C5 sing N N 156 V71 O5 C1 sing N N 157 V71 C5 C4 sing N N 158 V71 C4 C3 sing N N 159 V71 C1 C2 sing N N 160 V71 C1 O1 sing N N 161 V71 C2 C3 sing N N 162 V71 C2 N2 sing N N 163 V71 O11 C11 sing N N 164 V71 C3 O3 sing N N 165 V71 O1 C10 sing N N 166 V71 C10 C11 sing N N 167 V71 C10 C9 sing N N 168 V71 N9 C9 sing N N 169 V71 C11 C12 sing N N 170 V71 C12 O12 sing N N 171 V71 C12 C7 sing N N 172 V71 C9 C8 sing N N 173 V71 C8 C7 sing N N 174 V71 C7 N7 sing N N 175 V71 C1 H1 sing N N 176 V71 C10 H2A sing N N 177 V71 C11 H3A sing N N 178 V71 C12 H4A sing N N 179 V71 C2 H2 sing N N 180 V71 C3 H3 sing N N 181 V71 C4 H4 sing N N 182 V71 C5 H5 sing N N 183 V71 C6 H61 sing N N 184 V71 C6 H62 sing N N 185 V71 C7 H11 sing N N 186 V71 C8 H12 sing N N 187 V71 C8 H13 sing N N 188 V71 C9 H14 sing N N 189 V71 N2 H15 sing N N 190 V71 N2 H16 sing N N 191 V71 N6 H18 sing N N 192 V71 N6 H19 sing N N 193 V71 N7 H21 sing N N 194 V71 N7 H22 sing N N 195 V71 N9 H24 sing N N 196 V71 N9 H25 sing N N 197 V71 O11 H27 sing N N 198 V71 O12 H28 sing N N 199 V71 O3 HO3 sing N N 200 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 6JBF 'double helix' 6JBF 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 3 1_555 B C 23 1_555 -0.329 -0.026 -0.235 -5.157 -9.846 7.888 1 A_G3:C46_B A 3 ? B 46 ? 19 1 1 A C 4 1_555 B G 22 1_555 0.039 -0.136 -0.068 4.769 -9.466 1.169 2 A_C4:G45_B A 4 ? B 45 ? 19 1 1 A G 5 1_555 B C 21 1_555 -0.183 -0.016 0.260 4.872 -19.329 8.695 3 A_G5:C44_B A 5 ? B 44 ? 19 1 1 A U 6 1_555 B U 20 1_555 2.250 -1.331 0.123 -2.248 -16.838 10.137 4 A_U6:U43_B A 6 ? B 43 ? 16 1 1 A C 7 1_555 B G 19 1_555 0.144 -0.201 -0.420 -0.149 -0.546 2.741 5 A_C7:G42_B A 7 ? B 42 ? 19 1 1 A C 9 1_555 B G 16 1_555 0.556 -0.257 0.030 7.095 -19.794 1.715 6 A_C9:G39_B A 9 ? B 39 ? 19 1 1 A G 10 1_555 B C 15 1_555 -0.345 -0.198 -0.053 -1.808 -13.872 -0.191 7 A_G10:C38_B A 10 ? B 38 ? 19 1 1 A C 11 1_555 B G 14 1_555 0.376 -0.221 -0.012 4.869 -12.767 2.855 8 A_C11:G37_B A 11 ? B 37 ? 19 1 1 A C 12 1_555 B G 13 1_555 0.471 -0.011 -0.056 6.936 -10.077 4.400 9 A_C12:G36_B A 12 ? B 36 ? 19 1 1 A G 13 1_555 B C 12 1_555 -0.145 -0.032 -0.312 -8.779 -11.703 3.562 10 A_G13:C35_B A 13 ? B 35 ? 19 1 1 A G 14 1_555 B C 11 1_555 -0.479 -0.291 -0.117 -8.924 -7.583 0.893 11 A_G14:C34_B A 14 ? B 34 ? 19 1 1 A C 15 1_555 B G 10 1_555 0.078 -0.371 0.095 1.868 -7.322 -4.608 12 A_C15:G33_B A 15 ? B 33 ? 19 1 1 A G 16 1_555 B C 9 1_555 -0.264 -0.086 0.014 -2.447 -17.274 2.547 13 A_G16:C32_B A 16 ? B 32 ? 19 1 1 A A 18 1_555 B A 8 1_555 -2.959 1.685 -0.746 35.605 -4.054 -10.372 14 A_A18:A31_B A 18 ? B 31 ? ? ? 1 A G 19 1_555 B C 7 1_555 0.223 -0.141 0.173 9.077 -2.540 5.016 15 A_G19:C30_B A 19 ? B 30 ? 19 1 1 A U 20 1_555 B U 6 1_555 -1.878 -1.730 0.115 5.470 -12.320 15.359 16 A_U20:U29_B A 20 ? B 29 ? 16 1 1 A C 21 1_555 B G 5 1_555 0.512 -0.332 0.139 2.085 -15.881 6.029 17 A_C21:G28_B A 21 ? B 28 ? 19 1 1 A G 22 1_555 B C 4 1_555 -0.135 -0.103 0.105 -6.554 -6.006 -0.109 18 A_G22:C27_B A 22 ? B 27 ? 19 1 1 A C 23 1_555 B G 3 1_555 0.509 -0.039 0.258 9.377 -2.400 6.151 19 A_C23:G26_B A 23 ? B 26 ? 19 1 1 C G 3 1_555 D C 23 1_555 0.335 -0.202 0.220 1.017 -10.612 3.312 20 C_G49:C92_D C 49 ? D 92 ? 19 1 1 C C 4 1_555 D G 22 1_555 0.106 -0.305 -0.069 6.005 -10.363 2.368 21 C_C50:G91_D C 50 ? D 91 ? 19 1 1 C G 5 1_555 D C 21 1_555 0.044 -0.165 0.052 -6.786 -22.621 5.425 22 C_G51:C90_D C 51 ? D 90 ? 19 1 1 C U 6 1_555 D U 20 1_555 2.230 -1.676 0.312 -11.938 -18.298 2.947 23 C_U52:U89_D C 52 ? D 89 ? 16 1 1 C C 7 1_555 D G 19 1_555 0.251 -0.071 0.353 -10.050 -13.430 -2.600 24 C_C53:G88_D C 53 ? D 88 ? 19 1 1 C A 8 1_555 D A 18 1_555 2.490 1.701 0.350 -5.475 -2.680 -6.349 25 C_A54:A87_D C 54 ? D 87 ? ? 1 1 C C 9 1_555 D G 16 1_555 -0.112 -0.081 0.142 4.548 -15.767 -1.803 26 C_C55:G85_D C 55 ? D 85 ? 19 1 1 C G 10 1_555 D C 15 1_555 -0.209 -0.209 0.296 5.752 -8.318 0.912 27 C_G56:C84_D C 56 ? D 84 ? 19 1 1 C C 11 1_555 D G 14 1_555 -0.218 -0.272 0.257 5.729 -9.623 1.190 28 C_C57:G83_D C 57 ? D 83 ? 19 1 1 C C 12 1_555 D G 13 1_555 0.330 -0.100 -0.039 7.937 -9.691 2.798 29 C_C58:G82_D C 58 ? D 82 ? 19 1 1 C G 13 1_555 D C 12 1_555 0.065 -0.220 0.208 -0.098 -16.046 3.286 30 C_G59:C81_D C 59 ? D 81 ? 19 1 1 C G 14 1_555 D C 11 1_555 -0.752 -0.275 0.292 -6.601 -13.431 2.036 31 C_G60:C80_D C 60 ? D 80 ? 19 1 1 C C 15 1_555 D G 10 1_555 0.318 -0.091 0.182 -3.099 -14.799 3.886 32 C_C61:G79_D C 61 ? D 79 ? 19 1 1 C G 16 1_555 D C 9 1_555 0.321 -0.199 0.265 -0.729 -12.678 0.750 33 C_G62:C78_D C 62 ? D 78 ? 19 1 1 C A 18 1_555 D A 8 1_555 -2.951 1.227 0.404 1.533 -4.841 19.276 34 C_A64:A77_D C 64 ? D 77 ? ? 1 1 C G 19 1_555 D C 7 1_555 -0.733 0.123 0.404 8.796 -0.997 4.992 35 C_G65:C76_D C 65 ? D 76 ? 19 1 1 C U 20 1_555 D U 6 1_555 -1.002 -1.626 0.120 9.833 -13.007 -6.713 36 C_U66:U75_D C 66 ? D 75 ? 16 1 1 C C 21 1_555 D G 5 1_555 0.414 -0.268 -0.062 8.847 -21.279 2.772 37 C_C67:G74_D C 67 ? D 74 ? 19 1 1 C G 22 1_555 D C 4 1_555 -0.200 -0.175 -0.122 -15.769 -19.989 0.054 38 C_G68:C73_D C 68 ? D 73 ? 19 1 1 C C 23 1_555 D G 3 1_555 0.527 -0.035 0.444 -17.757 -10.613 3.446 39 C_C69:G72_D C 69 ? D 72 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 3 1_555 B C 23 1_555 A C 4 1_555 B G 22 1_555 -0.255 -0.891 2.995 -0.276 6.885 31.337 -2.712 0.417 2.745 12.556 0.503 32.067 1 AA_G3C4:G45C46_BB A 3 ? B 46 ? A 4 ? B 45 ? 1 A C 4 1_555 B G 22 1_555 A G 5 1_555 B C 21 1_555 0.779 -1.645 2.998 -2.417 15.993 27.462 -5.283 -1.766 1.729 30.559 4.618 31.792 2 AA_C4G5:C44G45_BB A 4 ? B 45 ? A 5 ? B 44 ? 1 A G 5 1_555 B C 21 1_555 A U 6 1_555 B U 20 1_555 0.249 -1.089 3.429 1.300 9.016 43.850 -2.269 -0.206 3.163 11.921 -1.718 44.740 3 AA_G5U6:U43C44_BB A 5 ? B 44 ? A 6 ? B 43 ? 1 A U 6 1_555 B U 20 1_555 A C 7 1_555 B G 19 1_555 -0.190 -2.432 3.104 4.412 5.292 22.938 -7.345 1.693 2.411 12.939 -10.787 23.937 4 AA_U6C7:G42U43_BB A 6 ? B 43 ? A 7 ? B 42 ? 1 A C 9 1_555 B G 16 1_555 A G 10 1_555 B C 15 1_555 -0.430 -1.761 3.229 -0.491 15.953 30.405 -5.159 0.664 2.080 28.116 0.866 34.252 5 AA_C9G10:C38G39_BB A 9 ? B 39 ? A 10 ? B 38 ? 1 A G 10 1_555 B C 15 1_555 A C 11 1_555 B G 14 1_555 0.334 -1.345 3.068 0.134 2.642 34.452 -2.641 -0.543 2.961 4.453 -0.226 34.551 6 AA_G10C11:G37C38_BB A 10 ? B 38 ? A 11 ? B 37 ? 1 A C 11 1_555 B G 14 1_555 A C 12 1_555 B G 13 1_555 -0.130 -1.683 3.317 -0.226 4.631 28.903 -4.307 0.210 3.018 9.203 0.449 29.264 7 AA_C11C12:G36G37_BB A 11 ? B 37 ? A 12 ? B 36 ? 1 A C 12 1_555 B G 13 1_555 A G 13 1_555 B C 12 1_555 0.054 -1.779 3.528 0.895 12.531 28.335 -5.685 0.067 2.533 24.153 -1.725 30.943 8 AA_C12G13:C35G36_BB A 12 ? B 36 ? A 13 ? B 35 ? 1 A G 13 1_555 B C 12 1_555 A G 14 1_555 B C 11 1_555 -0.557 -1.891 3.143 -2.639 9.614 31.443 -4.783 0.584 2.509 17.207 4.723 32.948 9 AA_G13G14:C34C35_BB A 13 ? B 35 ? A 14 ? B 34 ? 1 A G 14 1_555 B C 11 1_555 A C 15 1_555 B G 10 1_555 0.068 -1.261 3.105 0.237 8.008 31.818 -3.479 -0.084 2.716 14.325 -0.425 32.786 10 AA_G14C15:G33C34_BB A 14 ? B 34 ? A 15 ? B 33 ? 1 A C 15 1_555 B G 10 1_555 A G 16 1_555 B C 9 1_555 0.834 -1.641 3.250 2.863 13.992 28.618 -5.262 -1.050 2.291 26.335 -5.389 31.917 11 AA_C15G16:C32G33_BB A 15 ? B 33 ? A 16 ? B 32 ? 1 A G 16 1_555 B C 9 1_555 A A 18 1_555 B A 8 1_555 -3.472 -0.113 3.093 13.586 23.082 35.882 -1.802 5.556 1.434 32.490 -19.124 44.510 12 AA_G16A18:A31C32_BB A 16 ? B 32 ? A 18 ? B 31 ? 1 A A 18 1_555 B A 8 1_555 A G 19 1_555 B C 7 1_555 0.467 -1.750 3.760 -15.055 15.751 42.904 -3.468 -1.829 2.700 20.065 19.179 47.885 13 AA_A18G19:C30A31_BB A 18 ? B 31 ? A 19 ? B 30 ? 1 A G 19 1_555 B C 7 1_555 A U 20 1_555 B U 6 1_555 0.090 -2.415 3.055 -5.076 6.564 24.965 -6.792 -1.343 2.293 14.675 11.348 26.287 14 AA_G19U20:U29C30_BB A 19 ? B 30 ? A 20 ? B 29 ? 1 A U 20 1_555 B U 6 1_555 A C 21 1_555 B G 5 1_555 -0.482 -1.206 3.363 -1.513 6.181 42.769 -2.245 0.506 3.181 8.420 2.061 43.218 15 AA_U20C21:G28U29_BB A 20 ? B 29 ? A 21 ? B 28 ? 1 A C 21 1_555 B G 5 1_555 A G 22 1_555 B C 4 1_555 -0.855 -2.069 3.295 0.997 11.271 25.254 -6.721 2.001 2.156 24.283 -2.149 27.636 16 AA_C21G22:C27G28_BB A 21 ? B 28 ? A 22 ? B 27 ? 1 A G 22 1_555 B C 4 1_555 A C 23 1_555 B G 3 1_555 0.555 -1.401 2.935 0.166 8.162 30.852 -3.804 -0.985 2.495 15.016 -0.306 31.888 17 AA_G22C23:G26C27_BB A 22 ? B 27 ? A 23 ? B 26 ? 1 C G 3 1_555 D C 23 1_555 C C 4 1_555 D G 22 1_555 0.180 -1.469 3.150 -0.146 4.734 30.038 -3.682 -0.371 2.889 9.063 0.279 30.401 18 CC_G49C50:G91C92_DD C 49 ? D 92 ? C 50 ? D 91 ? 1 C C 4 1_555 D G 22 1_555 C G 5 1_555 D C 21 1_555 0.370 -1.756 3.431 -0.207 14.015 27.824 -5.766 -0.728 2.300 27.077 0.400 31.093 19 CC_C50G51:C90G91_DD C 50 ? D 91 ? C 51 ? D 90 ? 1 C G 5 1_555 D C 21 1_555 C U 6 1_555 D U 20 1_555 -0.236 -1.129 3.310 -1.728 7.601 46.451 -2.030 0.155 3.106 9.557 2.173 47.064 20 CC_G51U52:U89C90_DD C 51 ? D 90 ? C 52 ? D 89 ? 1 C U 6 1_555 D U 20 1_555 C C 7 1_555 D G 19 1_555 0.348 -1.670 2.790 8.236 9.453 30.238 -4.268 0.515 2.201 17.220 -15.003 32.678 21 CC_U52C53:G88U89_DD C 52 ? D 89 ? C 53 ? D 88 ? 1 C C 7 1_555 D G 19 1_555 C A 8 1_555 D A 18 1_555 -1.807 -1.668 3.175 4.028 10.508 24.337 -5.854 4.764 1.977 23.392 -8.967 26.777 22 CC_C53A54:A87G88_DD C 53 ? D 88 ? C 54 ? D 87 ? 1 C A 8 1_555 D A 18 1_555 C C 9 1_555 D G 16 1_555 2.804 -0.597 4.536 -11.766 28.442 39.327 -3.340 -4.432 2.673 36.300 15.017 49.562 23 CC_A54C55:G85A87_DD C 54 ? D 87 ? C 55 ? D 85 ? 1 C C 9 1_555 D G 16 1_555 C G 10 1_555 D C 15 1_555 -0.049 -1.686 3.125 -3.303 8.477 30.160 -4.516 -0.458 2.559 15.843 6.174 31.472 24 CC_C55G56:C84G85_DD C 55 ? D 85 ? C 56 ? D 84 ? 1 C G 10 1_555 D C 15 1_555 C C 11 1_555 D G 14 1_555 -0.164 -1.548 3.226 -0.788 5.821 31.747 -3.761 0.162 2.907 10.528 1.426 32.272 25 CC_G56C57:G83C84_DD C 56 ? D 84 ? C 57 ? D 83 ? 1 C C 11 1_555 D G 14 1_555 C C 12 1_555 D G 13 1_555 0.471 -1.101 3.177 4.507 3.688 36.326 -2.229 -0.155 3.089 5.869 -7.172 36.774 26 CC_C57C58:G82G83_DD C 57 ? D 83 ? C 58 ? D 82 ? 1 C C 12 1_555 D G 13 1_555 C G 13 1_555 D C 12 1_555 -0.414 -1.677 3.326 -0.131 13.385 28.835 -5.307 0.735 2.339 25.233 0.246 31.731 27 CC_C58G59:C81G82_DD C 58 ? D 82 ? C 59 ? D 81 ? 1 C G 13 1_555 D C 12 1_555 C G 14 1_555 D C 11 1_555 -0.254 -1.462 3.241 -3.831 9.870 28.616 -4.602 -0.224 2.616 19.160 7.436 30.473 28 CC_G59G60:C80C81_DD C 59 ? D 81 ? C 60 ? D 80 ? 1 C G 14 1_555 D C 11 1_555 C C 15 1_555 D G 10 1_555 0.170 -0.991 3.189 -0.202 5.302 39.683 -2.028 -0.270 3.036 7.768 0.295 40.022 29 CC_G60C61:G79C80_DD C 60 ? D 80 ? C 61 ? D 79 ? 1 C C 15 1_555 D G 10 1_555 C G 16 1_555 D C 9 1_555 0.285 -1.556 3.040 -0.532 9.247 31.190 -4.176 -0.589 2.484 16.741 0.963 32.503 30 CC_C61G62:C78G79_DD C 61 ? D 79 ? C 62 ? D 78 ? 1 C G 16 1_555 D C 9 1_555 C A 18 1_555 D A 8 1_555 -2.000 -1.228 4.165 9.110 24.713 41.864 -3.588 3.184 2.634 31.172 -11.491 49.143 31 CC_G62A64:A77C78_DD C 62 ? D 78 ? C 64 ? D 77 ? 1 C A 18 1_555 D A 8 1_555 C G 19 1_555 D C 7 1_555 -0.756 -1.296 2.958 -4.459 8.432 31.350 -3.567 0.672 2.611 15.171 8.022 32.735 32 CC_A64G65:C76A77_DD C 64 ? D 77 ? C 65 ? D 76 ? 1 C G 19 1_555 D C 7 1_555 C U 20 1_555 D U 6 1_555 -0.359 -2.026 3.082 -0.471 8.100 30.862 -4.964 0.579 2.488 14.900 0.866 31.885 33 CC_G65U66:U75C76_DD C 65 ? D 76 ? C 66 ? D 75 ? 1 C U 20 1_555 D U 6 1_555 C C 21 1_555 D G 5 1_555 0.356 -1.334 3.241 0.755 6.305 42.749 -2.408 -0.412 3.030 8.592 -1.029 43.196 34 CC_U66C67:G74U75_DD C 66 ? D 75 ? C 67 ? D 74 ? 1 C C 21 1_555 D G 5 1_555 C G 22 1_555 D C 4 1_555 -0.257 -1.780 3.563 1.019 17.228 29.841 -5.575 0.587 2.226 30.461 -1.802 34.373 35 CC_C67G68:C73G74_DD C 67 ? D 74 ? C 68 ? D 73 ? 1 C G 22 1_555 D C 4 1_555 C C 23 1_555 D G 3 1_555 0.341 -1.222 3.220 -2.410 9.777 38.906 -2.825 -0.754 2.819 14.387 3.547 40.139 36 CC_G68C69:G72C73_DD C 68 ? D 73 ? C 69 ? D 72 ? # _pdbx_audit_support.funding_organization 'Ministry of Education, Culture, Sports, Science and Technology (Japan)' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number 26860025 _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranoside' V71 3 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1J7T _pdbx_initial_refinement_model.details ? # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #